Hepatitis C viruses (HCV) have been found to be the major cause of non-A, non-B hepatitis. The sequences of cDNA clones covering the complete genome of several prototype isolates have been determined and include complete prototype genomes of the HCV genotypes 1a (e.g., GenBank accession number AF009606), 1b (e.g., GenBank accession number AB016785), 1c (e.g., GenBank accession number D14853), 2a (e.g., GenBank accession number AB047639), 2b (e.g., GenBank accession number AB030907), 2c (e.g., GenBank accession number D50409) 2k (e.g., GenBank accession number AB031663), 3a (e.g., GenBank accession number AF046866), 3b (e.g., GenBank accession number D49374), 4a (e.g., GenBank accession number Y11604), 5a (e.g., GenBank accession number AF064490), 6a (e.g., GenBank accession number Y12083), 6b (e.g., GenBank accession number D84262), 7b (e.g., GenBank accession number D84263), 8b (e.g., GenBank accession number D84264), 9a (e.g., GenBank accession number D84265), 10a (e.g., GenBank accession number D63821) and 11a (e.g., GenBank accession number D63822). The first complete HCV genomes ever characterized were later classified as HCV genotypes 1a (HCV-1; Choo et al. 1991), 1b (HCV-J; Kato et al. 1990), 2a (HC-J6; Okamoto et al. 1991) and 2b (HC-J8; Okamoto et al. 1992). Comparison of these isolates shows that the variability in nucleotide sequences can be used to distinguish at least 2 different genotypes, type 1 (HCV-1 and HCV-J) and type 2 (HC-J6 and HC-J8), with an average homology of about 68%. Within each type, at least two subtypes exist (e.g. type 1 represented by type 1a HCV-1 and type 1b HCV-J), having an average homology of about 79%. HCV genomes belonging to the same subtype show average homologies of more than 90% (Okamoto et al. 1992). However, the partial nucleotide sequence of the NS5 region of the HCV-T isolates showed at most 67% homology with the previously published sequences, indicating the existence of yet another HCV type (Mori et al. 1992). Parts of the 5′ untranslated region (UR, UTR or non-coding region, NCR), core, NS3, and NS5 regions of this type 3 have been published, further establishing the similar evolutionary distances between the 3 major genotypes and their subtypes (Chan et al. 1992). Type 4 was subsequently discovered (Stuyver et al. 1993b; Simmonds et al., 1993a; Bukh et al., 1993; Stuyver et al., 1994a) followed by type 5 (Stuyver et al. 1993b; Simmonds et al. 1993c; Bukh et al. 1993; Stuyver et al. 1994b) and type 6 HCV groups (Bukh et al. 1993; Simmonds et al. 1993c). An overview of the different HCV genotype classification systems used in the past and (part of) the current nomenclature system is given in Table 3. The nomenclature system proposed by the inventors of the present application (Arabic number for major type followed by lower-case Roman letter for each subtype) has now been accepted by scientists worldwide (Simmonds et al. 1994). At the moment, 11 genotypes of HCV are known, which can be classified into 6 Clades. Thus, HCV genotypes 1, 2, 4, and 5 are identified as clades 1, 2, 4 and 5, respectively; HCV genotypes 3 and 10 belong to clade 3; and HCV genotypes 6, 7, 8, 9 and 11 are members of clade 6 (Robertson et al. 1998; see also FIG. 3 of the present invention). The current classification system is based on a threefold hierarchy as will be described in detail furtheron. Basically, the classification system distinguishes, based on percentage of mutual homologies between sequences, between:                HCV isolates belonging to different types;        HCV isolates belonging to the same type but to a different subtype; and        HCV isolates belonging to the same subtype (Maertens and Stuyver 1997).        
Nucleic acid and amino acid sequences of HCV genotypes 1 to 11 have been disclosed not only in public databases but also in, e.g., International Patent Publications WO94/12670, WO94/25601, and WO96/13590.